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Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. coiaf: Directly estimating complexity of infection with allele frequencies. PLoS Comput Biol 2023; 19:e1010247. [PMID: 37294835 PMCID: PMC10310041 DOI: 10.1371/journal.pcbi.1010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2023] [Accepted: 05/01/2023] [Indexed: 06/11/2023] Open
Abstract
In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
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Affiliation(s)
- Aris Paschalidis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Oliver J. Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robert Verity
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
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Kojom Foko LP, Hawadak J, Kouemo Motse FD, Eboumbou Moukoko CE, Kamgain Mawabo L, Pande V, Singh V. Non-falciparum species and submicroscopic infections in three epidemiological malaria facets in Cameroon. BMC Infect Dis 2022; 22:900. [PMID: 36460990 PMCID: PMC9718470 DOI: 10.1186/s12879-022-07901-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND There are growing reports on the prevalence of non-falciparum species and submicroscopic infections in sub-Saharan African countries but little information is available from Cameroon. METHODS A hospital-based cross-sectional study was carried out in four towns (Douala, Maroua, Mayo-Oulo, and Pette) from three malaria epidemiological strata (Forest, Sahelian, and Soudanian) of Cameroon. Malaria parasites were detected by Giemsa light microscopy and polymerase chain reaction (PCR) assay. Non-falciparum isolates were characterized and their 18S gene sequences were BLASTed for confirmatory diagnosis. RESULTS PCR assay detected malaria parasites in 82.4% (98/119) patients, among them 12.2% (12/98) were asymptomatic cases. Three Plasmodium species viz. P. falciparum, P. ovale curtisi and P. vivax, and two co-infection types (P. falciparum + P. vivax and P. falciparum + P. ovale curtisi) were found. The remaining infections were mono-infections with either P. falciparum or P. ovale curtisi. All non-falciparum infections were symptomatic and microscopic. The overall proportion of submicroscopic infections was 11.8% (14/119). Most asymptomatic and submicroscopic infection cases were self-medicated with antimalarial drugs and/or medicinal plants. On analysis, P. ovale curtisi sequences were found to be phylogenetically closer to sequences from India while P. vivax isolates appeared closer to those from Nigeria, India, and Cameroon. No G6PD-d case was found among non-falciparum infections. CONCLUSIONS This study confirms our previous work on circulation of P. vivax and P. ovale curtisi and the absence of P. knowlesi in Cameroon. More studies are needed to address non-falciparum malaria along with submicroscopic infections for effective malaria management and control in Cameroon.
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Affiliation(s)
- Loick Pradel Kojom Foko
- grid.419641.f0000 0000 9285 6594ICMR-National Institute of Malaria Research, Dwarka, New-Delhi 110077 India ,grid.411155.50000 0001 1533 858XDepartment of Biotechnology, Kumaun University, Bhimtal, Uttarakhand 263001 India
| | - Joseph Hawadak
- grid.419641.f0000 0000 9285 6594ICMR-National Institute of Malaria Research, Dwarka, New-Delhi 110077 India ,grid.411155.50000 0001 1533 858XDepartment of Biotechnology, Kumaun University, Bhimtal, Uttarakhand 263001 India
| | - Francine Dorgelesse Kouemo Motse
- grid.29273.3d0000 0001 2288 3199Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, 63, Buea, Cameroon
| | - Carole Else Eboumbou Moukoko
- grid.413096.90000 0001 2107 607XDepartment of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, 24157 Douala, Cameroon ,Malaria Research Unit, Centre Pasteur Cameroon, 1274 Yaoundé, Cameroon ,grid.413096.90000 0001 2107 607XLaboratory of Parasitology, Mycology and Virology, Postgraduate Training Unit for Health Sciences, Postgraduate School for Pure and Applied Sciences, The University of Douala, 24157 Douala, Cameroon
| | | | - Veena Pande
- grid.411155.50000 0001 1533 858XDepartment of Biotechnology, Kumaun University, Bhimtal, Uttarakhand 263001 India
| | - Vineeta Singh
- grid.419641.f0000 0000 9285 6594ICMR-National Institute of Malaria Research, Dwarka, New-Delhi 110077 India
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Futagbi G, Otu PS, Abdul-Rahman M, Aidoo EK, Lo AC, Gyan BA, Afrane YA, Amoah LE. Association of TNF-Alpha, MBL2, NOS2, and G6PD with Malaria Outcomes in People in Southern Ghana. Genet Res (Camb) 2022; 2022:6686406. [PMID: 35291755 PMCID: PMC8901335 DOI: 10.1155/2022/6686406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background One major issue that has set back the gains of the numerous malaria control interventions that national malaria control programs have implemented is asymptomatic malaria. Certain host genetic factors are known to influence symptomatic malaria; however, not much is known about how host genetics influences the acquisition of asymptomatic malaria. Methods Genomic DNA was extracted from whole blood collected from 60 symptomatic and 149 nonfebrile (asymptomatic, N = 109, and uninfected, N = 40) volunteers aged between 2 and 69 years from a high (Obom) and a low (Asutsuare) malaria transmission setting in Southern Ghana. Restriction fragment length polymorphism (RFLP) was used to determine polymorphisms at the MBL2 54, TNF-α 308, NOS2 954, and G6PD 202/376 gene loci. Results Polymorphisms at the MBL2 54 and TNF-α 308 loci were significantly different amongst the three categories of volunteers in both Asutsuare (p = 0.006) and Obom (p=0.05). In Asutsuare, a low malaria transmission area, the allele G has significantly higher odds (3.15) of supporting asymptomatic malaria as against symptomatic malaria. There were significantly higher odds of TNF-α genotype GA being associated with symptomatic malaria as against asymptomatic malaria in both sites, Obom (p=0.027) and Asutsuare (p=0.027). The allele B of the G6PD gene was more prevalent in symptomatic rather than asymptomatic parasite-infected individuals in both Obom (p=0.001) and Asutsuare (p=0.003). Conclusion Individuals in Southern Ghana carrying the TNF-α 308 GA genotype are more likely to exhibit symptoms of malaria when infected with the malaria parasite as opposed to harboring an asymptomatic infection. Also, the B allele of the G6PD gene is likely to prevent a P. falciparum-infected person from exhibiting symptoms and thereby promote asymptomatic parasite carriage.
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Affiliation(s)
- Godfred Futagbi
- Department of Animal Biology and Conservation Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Paulina S Otu
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Mubarak Abdul-Rahman
- Department of Pathology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Ebenezer K Aidoo
- Department of Medical Laboratory, Accra Technical University, Accra, Ghana
| | - Aminata C Lo
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medical Parasitology, Faculty of Medicine, University Cheikh Anta Diop, Dakar, Senegal
| | - Ben A Gyan
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Yaw A Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Linda E Amoah
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West Africa Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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Acquah FK, Donu D, Bredu D, Eyia-Ampah S, Amponsah JA, Quartey J, Obboh EK, Mawuli BA, Amoah LE. Asymptomatic carriage of Plasmodium falciparum by individuals with variant blood groups and haemoglobin genotypes in southern Ghana. Malar J 2020; 19:217. [PMID: 32576186 PMCID: PMC7310487 DOI: 10.1186/s12936-020-03299-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background The ABO and the Rhesus blood group systems, as well as various abnormal haemoglobin (Hb) variants (haemoglobinopathies) are known to influence malaria parasite carriage and disease severity in individuals living in malaria endemic areas. This study identified the blood group and Hb variant distribution and Plasmodium falciparum infection status of afebrile individuals living in southern Ghana. Methods Afebrile participants were recruited from Obom (358) in the Greater Accra Region and Ewim (100) and Simiw (329) in the Central Region of Ghana. Venous blood (1 ml) was collected into EDTA vacutainer tubes. Three 20 μl drops of blood were used for blood group analysis using the tile method. Another 500 μl aliquot was used for the qualitative sickling test using sodium metabisulphite and haemoglobin electrophoresis. Genomic DNA was extracted from 100 μl of whole blood and used in P. falciparum species-specific PCR. Results The most abundant blood group and abnormal haemoglobin variant in both sites was blood group O + (47.4%) and HbAS (15.8%). A total of 13 (1.7%) of the participants had full haemoglobinopathies (SS, SC and CC), whilst 196 (25.4%) were carriers (AS and AC). Although there was a significantly higher prevalence of sickling positive participants from the Central Region, genotyping identified a similar prevalence of each of the abnormal haemoglobin genes in both sites. Asymptomatic parasite carriage estimated by PCR was 40.9% in the Central Region and 41.8% in the Greater Accra Region. Conclusions Asymptomatic carriage of P. falciparum parasite in the study population was not associated with any particular blood group variant or haemoglobin genotype.
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Affiliation(s)
- Festus K Acquah
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Volta Road, Legon, P.O. Box LG 54, Accra, Ghana
| | - Dickson Donu
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana
| | - Dorcas Bredu
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana
| | - Sophia Eyia-Ampah
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana
| | - Jones A Amponsah
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana
| | - Joseph Quartey
- Parasitology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana
| | - Evans K Obboh
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Bernice A Mawuli
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Volta Road, Legon, P.O. Box LG 54, Accra, Ghana
| | - Linda E Amoah
- Immunology Department, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, P. O. Box LG 581, Accra, Ghana. .,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Volta Road, Legon, P.O. Box LG 54, Accra, Ghana.
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Stresman G, Bousema T, Cook J. Malaria Hotspots: Is There Epidemiological Evidence for Fine-Scale Spatial Targeting of Interventions? Trends Parasitol 2019; 35:822-834. [PMID: 31474558 DOI: 10.1016/j.pt.2019.07.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
As data at progressively granular spatial scales become available, the temptation is to target interventions to areas with higher malaria transmission - so-called hotspots - with the aim of reducing transmission in the wider community. This paper reviews literature to determine if hotspots are an intrinsic feature of malaria epidemiology and whether current evidence supports hotspot-targeted interventions. Hotspots are a consistent feature of malaria transmission at all endemicities. The smallest spatial unit capable of supporting transmission is the household, where peri-domestic transmission occurs. Whilst the value of focusing interventions to high-burden areas is evident, there is currently limited evidence that local-scale hotspots fuel transmission. As boundaries are often uncertain, there is no conclusive evidence that hotspot-targeted interventions accelerate malaria elimination.
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Affiliation(s)
- Gillian Stresman
- Infection Biology Department, London School of Hygiene and Tropical Medicine, London, UK.
| | - Teun Bousema
- Radboud University Medical Centre, Department of Microbiology, HB Nijmegen, The Netherlands.
| | - Jackie Cook
- Medical Research Council (MRC) Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
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Iro A, Lamine MM, Lazoumar RH, Alkassoum I, Maman D, Laouali HAM, Doutchi M, Maiguizo S, Laminou IM. Transfusional Malaria and Associated Factors at the National Blood Transfusion Center of Niamey-Niger. J Trop Med 2019; 2019:7290852. [PMID: 31057629 PMCID: PMC6463555 DOI: 10.1155/2019/7290852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/19/2019] [Indexed: 12/21/2022] Open
Abstract
SUMMARY Problem. Transfusional malaria is an accidental transmission of Plasmodium via a blood transfusion. Its magnitude is underestimated and very little data on the assessment of this risk are available in Niger. OBJECTIVE This study aimed to determine the prevalence of plasmodial infection of blood bags at the National Blood Transfusion Center of Niamey (NBTC). METHODOLOGY A cross-sectional study to diagnose Plasmodium infection by microscopy and Rapid Diagnostic Test (RDT) was carried out during the rainy season (September to November 2015). Blood grouping was performed by the BETH-VINCENT technique. RESULTS One thousand three hundred and fifty-seven (1357) blood bags were collected. One hundred and fifty-seven (11.6%) of the donors were infected with Plasmodium by microscopy and 2.4% (9/369) by rapid diagnostic test. All infections were with P. falciparum (100%). The mean parasite density was 197 parasites/μL (SD=281; [80: 2000]). There were no significant differences in infection prevalence between the ABO blood groups (p = 0.3) or the rhesus positivity (p=08). There is also no significant difference in temporal (p = 0.1) and spatial (p = 0.6) distribution. CONCLUSION The transmission of transfusional malaria during the rainy season is a fact in Niger. Such risks were independent of the ABO blood type and positivity for the rhesus antigen. Pretransfusion diagnosis or posttransfusion therapy should be instituted to prevent it.
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Affiliation(s)
- Aminata Iro
- Faculté de Science de la Santé de l'Université de Niamey, Niger
| | | | | | | | - Daou Maman
- Faculté de Science de la Santé de l'Université de Niamey, Niger
- Hôpital National de Niamey, Niger
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